CCTS Informatics provides the resources and expertise (both bioinformatics and clinical informatics) to support biomedical collaboration and consultation across the translational research spectrum. We offer help with study design; access to summary, limited (de-identified), and fully identified data sets; innovative tools to support clinical, translational, and outcomes research; and data analytic services. Our vision is to build a vibrant community of collaborating informaticians not only across the CCTS Hub with its academic medical system, but also across the regional CCTS Partner Network and national CTSA Consortium.
-
Data Access and Support
Analyst-faciliated Data Access i2b2 Self-Service TriNetX Research™ National COVID Cohort Collaboration (N3C) ACT Network One Florida+ Data Type EHR, inclusively Significant* reflection
of EHR structured data
(e.g., labs, meds, diagnoses, procedures, billing codes and more)Limited Structured data (e.g., labs, meds, procedures, billings codes) Structured data related
to COVID-19 (e.g., labs, meds, procedures, billing codes)Structured data (labs, meds, procedures, billings codes) EHR, inclusively Who Can Access UAB Faculty and Staff CCTS based on IRB approval or policy UAB Faculty and Staff
CCTS PartnersUAB Faculty and Staff UAB Faculty, Staff and ***participating Institutions UAB Faculty and Staff UAB Faculty and Staff Patient Population UAB Medicine UAB Medicine UAB + over 70 HCOs UAB + over 50 HCOs CCTS Partners (coming soon) Select Health Systems in FL, GA and AL Results PHI / PII, HIPAA Limited Data (LDS)
Aggregate CountsHIPAA Limited Data
Aggregate CountsHIPAA Limited Data
Aggregate CountsHIPAA Limited Data Aggregate Counts Aggregate Counts HIPAA Limited Data (LDS),
Aggregate CountsDownloadable Yes (with assistance) Yes Yes (HIPAA LDS with approval) No Yes Yes (with assistance) IRB Requirement Approved Investigator-initiated protocol if PHI or LDS **No individual IRB
Approval requiredApproved Investigator-
initiated protocol for LDSApproved Investigator-initiated protocol **No individual IRB Approval required Approved Investigator-initiated protocol required Cost to Use CCTS/Informatics Instituted Supported; Budget in grants CCTS/Informatics
Institute SupportedFree preparatory to research; Budget in
grantsNo Charge CCTS/Informatics
Institute SupportedDetermined by project scope
Log in to DataLENS i2b2
LoginContact
CCTSN3C
LoginACT Network
LoginOneFlorida+
Front Door---------------------------------------------------------------------------------
EHR, Electronic Health Record; HCO, Healthcare Organization; PHI, Protected Health Information; PII, Personally identifiable information, HIPAA, Health Insurance Portability and Accountability Act; CTSA, Clinical and Translational Science Award(ee)
*Fact types include allergy data, billed charges, biospecimen data, blood pressure, BMI and waist, cancer registry, clinical diagnosis, consult orders, diagnosis-related group (DRG), encounter insurance, encounter service, height, weight, immunizations, lab panels, lab powerplans, labs, medications, microbiology, select powernotes, problems, procedures (CPTs, ICD9/10), radiology events, social history, surgery data, etc.
** Permitted Users, covered entities, and any Authorized Party on User's behalf listed in (Research Title/Grant Title) may use i2b2 self-service Limited Data Sets only for the purposes which shall be limited to research, public health activities, and health care operations as defined in the HIPAA Privacy Rule (per IRB protocol E160105006) and not for no other purpose.
*** Institutions listed on the N3C website https://covid.cd2h.org/enclave_DUA_signatories
For more complex data needs, including access to detailed data sets, investigators can submit a request to CCTS Informatics for support from an Electronic Data Warehouse (EDW) analyst. -
National COVID-19 Cohort Collaborative (N3C)
N3C is Open for Business. Learn How to Get Started.
*Click here to review the latest N3C updates.
The National COVID Cohort Collaborative (N3C) has created a large, centralized data resource available to the research community to study COVID-19 at a scale and statistical power not possible within any single institution. N3C has assembled a standardized collection of clinical, laboratory and diagnostic data from hospital electronic health records and health care plans across the country for analysis within an accessible, cloud-based data enclave. Here is how you can get involved:
- Secure IRB approval from your institution – submit a request for human subjects research exemption from your IRB (see template here). See also this example of the HIPAA Waiver Request.
- UAB Investigators, remember to connect your IRB approval request to the N3C research initiative. Here's how: The IRB EPortfolio contains this question: Does the project involve other agreements not identified by an OSP Assigned Number (e.g. Fee for Service)?“ Respond with text that includes the following information: " The N3C DUA corresponds to OSP# 000529456 and IRB-300005342, both led by CCTS Co-Director and UAB Informatics Institute Director, Dr. James Cimino.”
- On-board with the N3C data enclave – register for membership (ORCID ID required) and gain access to workstreams (e.g., Collaborative Analytics) to share how-to’s and solutions.
- Read the N3C Data User Code of Conduct.
- Create an account to access the N3C Data Enclave.
- Train Up! All users of the N3C Data Enclave are required to complete the 2020 Information Security, Counterintelligence, Privacy Awareness, Records Management Refresher, Emergency Preparedness Refresher. Users are also expected, but not required, to complete the Palantir Fundamentals training course available within an active N3C account.
- Prepare Information to submit a Data Use Request (DUR). Guided by this template, a DUR will need to be completed online upon accessing the enclave, requiring upload of your IRB approval letter.
The DUR and IRB approval letter can be submitted to N3C once the DUA is signed by the University. In the meantime, CCTS Partner Institutions are establishing the requisite Data Use Agreements with N3C. Multiple CCTS partner institutions have signed data use agreements in place and investigators at those sites are eligible to analyze data in the enclave: Click to view the full list of institutions with active DUAs.
Additional Resources:
These domain teams offer disciplinary opportunities for physician scientists. Coding skills not required!
N3C Fact Sheet
Getting started powerpoint presentation.
Access the N3C Helpdesk here.
Access the N3C Support Desk here.
Review the N3C Registration Checklist.
Check out the Frequently Asked Questions.
*On July 29th, CCTS and the UAB Informatics Institute hosted an N3C workshop aimed at preparing researchers to utilize this data resource. Access those presentation slides here. Recording of the event is available on the CCTS Video Channel. -
Informatics-based Scientific Gateways
Scientific Gateways are collaborative, multidisciplinary panel discussions – assembling expertise in informatics, design & methodology, and clinical investigation – to help investigators explore novel research directions. In partnership with the Center for Outcomes & Effectiveness Research, the CCTS supports two Scientific Gateway models dedicated to 1) ‘omics data analysis and 2) secondary clinical data analysis. To submit a project idea for consideration, fill in the relevant Informatics Gateway Request Form below or contact CCTS Research Commons at
This email address is being protected from spambots. You need JavaScript enabled to view it. or 205-996-4478. -
Bioinformatics
CCTS Bioinformatics provides data and analytic support for the following:
- Next Generation Sequence Analysis
- Microarray analysis
- Microbiome
- Data storage, management, and sharing plans
- Southeast SHRINE Consortium
- Educational tools and programs
-
Clinical Research Informatics
CCTS Clinical Research Informatics provides access to clinical data in the UAB Health System electronic health record to support:
- Enterprise Data Warehouse (EDW) Initiative
- Data access and exchange (via i2b2, SHRINE, and EDW analysts)
- Subject recruitment and retention tools—cohort feasibility, subject identification (with IRB approval), clinical phenotype
- Design and implementation of clinical research studies and secondary data analyses
- Targeting clinical trial opportunities (TriNetX)
- Informatics research (UAB Informatics Institute)
- Data science for population insights and "big data" integration
The All of Us Program opened the Researcher Workbench and is inviting researchers to apply for access to explore the initial dataset and tools. The Researcher Workbench is a secure, cloud-based platform that offers researchers an opportunity to execute rapid, hypothesis-driven research and build new methods for the future. -
Informatics Training
CCTS Informatics offers multiple opportunities throughout the year for investigators interested in learning more about informatics. Training events range from those to provide a general overview of concepts and to use informatics platforms (e.g., i2b2) to understand the language to deeper exploration of principles to develop competency and expertise.
Note: PRS Beta is now the primary website for Protocol Registration. For more information on the PRS transition, visit the Modernization Transition Top Questions. View our PRS Beta Site Videos and PRS Beta Site Step-By-Step Guide (PDF) to help with this transition.
Questions? Email
Log In to PRS: https://register.clinicaltrials.gov/
Need an account, advice, or help? Contact:
Helpful Hints:
|
Resources:
|
The National Center for Advancing Translational Science (NCATS) requires that we track and report on certain categories of research. Below we list and define these categories. Questions? Contact
HIV/AIDS Research – For more information, please see the UAB Center for AIDS Research.
Clinical Trials – (NIH Definition) A research study in which one or more human subjects are prospectively assigned to one or more interventions (which may include placebo or other control) to evaluate the effects of those interventions on health-related biomedical or behavioral outcomes.
Pediatric Research – Clinical research initiatives that either involve subjects younger than 19 and/or address aspects of a disease that is prevalent in children.
Disparities Research – Disparities Research examines differences in the incidence, prevalence, mortality, and burden of diseases and other adverse health conditions that exist among specific population groups. These may include a complex set of factors including biology, ancestry, geography & environment, social and economic issues, and age.
Special Populations – A special population is defined not only by biologic ancestry, but also by position across the lifespan (pediatrics, geriatrics), geography (urban, rural), socioeconomic status, and disproportionate disease burden of our region (e.g., cardio-metabolic, vascular and cancer-related diseases).
Cutting-Edge Knowledge
In addition to platform development for genomic studies, the CCTS Genomic Medicine Module supports training activities for learners of all stages and competencies. The CCTS offers both traditional and non-traditional approaches to genetics and genomics education and outreach including lectures, newsletters, workshops, retreats, symposia, professional development, and immersion courses, all of which are accessible to CCTS Partners via distance learning platforms.
Bioethics Forum
This annual event brings together researchers, bioethicists, students, and front-line research and clinical staff to discuss special ethics topics in research.
CCTS Drug Discovery Seminar Series
The CCTS also cosponsors the annual series with partner Southern Research.
Genetics and Genomics in Clinical Research
This week-long course, hosted by CCTS and the Heflin Center for Genomic Sciences in September, immerses investigators in the principles, technologies, and experimental approaches in genetics and genomics through both lecture and hands-on activities. Investigators from throughout the CCTS Partner Network are encouraged to participate (GTM is made available for long-distance attendees). Topics include:
- identifying genes related to family phenotypes that segregate in a Mendelian fashion
- developing a study to compare patterns of gene expression or methylation levels in normal vs pathological tissue
- preparing a genetics or genomics protocol involving human subjects for IRB review
- choosing a genotyping and next-generation sequencing platform
- using bioinformatics databases to analyze genomic data
Genomic Medicine Seminar Series
This biweekly seminar series will focus on case presentations or research seminars related to genomic medicine. The T32 trainees will present their research and their clinical cases from the Genomic Medicine Practicum at this conference along with faculty from UAB and HudsonAlpha. This series will bring together trainees, mentors, and life science experts and provide an excellent platform for debate among participants. The series will be held at UAB and HudsonAlpha alternatively and extended by WebEx to the other site.
HudsonAlpha Institute for Biotechnology Genomic Medicine Conference
The Genomic Medicine Conference is focused on advancing knowledge in the field of genomic medicine in a clinical care setting and empowering clinicians with the information they need to integrate genomics into medical practice.
UAB-HudsonAlpha Postdoc Training Program in Genomic Medicine
The Center for Genomic Medicine (CGM), a collaboration of CCTS Partners UAB and the HudsonAlpha Institute for Biotechnology, is accepting applications for a unique opportunity to research and validate new genomic approaches for clinical care, funded by a National Human Genome Research Institute T32 grant.
-
CCTS offers a wealth of learning and consultative opportunities to help students, trainees, faculty, staff, and clinicians develop valuable translational research skills and competencies at any stage of the career arc. Click here to learn more!
- To improve the rigor and reproducibility of your studies, learn how to access clinical data via our i2b2 tool, or find an informatics or BERD collaborator, visit our Research Commons page.
- To earn a certificate in mentoring or clinical and translational science, or apply to one of our mentored research career development programs, visit our Training Academy section.
- To master the principles of clinical research, improve a specific clinical trial implementation skill, enroll in our six-month clinical and translational science training program, or attend a quarterly Lunch & Learn to brush up on the latest regulatory requirements, visit our Clinical Translation training page.
- To find community based research partners, attend our annual Community Engagement Institute, or mentor a Community Health Innovation Awards (CHIA) applicant, visit our Engagement of Communities section.
- Learn more about entrepreneurship, the commercialization pathway, and team science by visiting our Innovation page.
Unprecedented Opportunity
The sequencing of the human genome has created an unprecedented opportunity to apply new knowledge and technology to improve human health. The goal of the CCTS Genomic & Precision Medicine Special Module is to connect clinical and translational researchers to expertise and capacity to undertake genetic and genomic investigation. In this way, the Network will accelerate discoveries in genomics and genomic medicine and will propel those discoveries into clinical application.
Building on the state-of-the-art technologic capacities and expertise at the Hub, HudsonAlpha Institute for Biotechnology (HudsonAlpha), and other CCTS Partners, the Genomic & Precision Medicine Module catalyzes rigorous genomic research and innovation through consultation with CCTS investigators in the design and implementation of studies, including advice regarding scientific strategy, appropriate use of technologies as well as data analysis. These experts also spearhead cutting-edge assay development, including single-cell genomics and advanced next-generation sequencing of nucleic acid species (e.g., miRNA), techniques that are made available to investigators throughout the Partner Network.
The Genomic & Precision Medicine Module also supports collaborative research initiatives:
Alabama Genome Health Initiative
The Alabama Genomic Health Initiative (AGHI) is one of the nation's first statewide efforts to harness the power of genomic analysis in helping identify those who are at risk for diseases for genomic abnormalities. The AGHI is funded by the State of Alabama as a genomics research program intended to engage a varied group of citizens from all 67 counties of the state. In collaboration with the HudsonAlpha Institute for Biotechnology in Huntsville, UAB Medicine provides genotyping or whole genome sequencing to 10,000 residents of Alabama free of charge. The AGHI is one of the nation’s first statewide efforts to harness the power of genomic analysis to help identify those at risk for certain genetic disorders and to provide a basis for continuing research into genetic contributors to health and disease.
All of Us Research Program
UAB, CCTS Partner Network Hub, launched the Southern Network of the All of Us Research Program on May 6, 2018. Since then, the network has enrolled over 7,000 participants in this historic initiative. All of Us, spearheaded by the National Institutes of Health, is a national program to accelerate health research and medical breakthroughs, enabling individualized prevention, treatment, and care for all of us. The overall aim nationally is to enroll 1 million or more volunteers and oversample communities that have been underrepresented in biomedical research to make the program the largest resource of its kind. UAB heads the Southern Network, comprising Alabama, Mississippi, and Louisiana, and is led by Bruce R. Korf, MD, PhD, the School of Medicine’s Chief Genomics Officer and CCTS Director of Genomic Medicine, and Cora E. Lewis, MD, Chair of the Department of Epidemiology in the School of Public Health.
South-Seq
South-Seq is a collaborative effort among CCTS Partner Network researchers and clinicians at the HudsonAlpha Institute for Biotechnology, the University of Alabama-Birmingham, and the University of Mississippi Medical Center. Newborns are enrolled that are suspected to have genetic disorders and are being cared for in nurseries in Alabama and Mississippi that are enriched for minority, rural, and underserved patients. Whole-genome sequencing is conducted to identify genetic variants that are contributing to the observed symptoms and which may provide diagnostic and prognostic information. South-Seq is exploring effective and ethical ways to communicate this information to parents. Major goals are to expand the reach of genomic testing to under-served communities in a safe, effective, and equitable manner. Learn more
Undiagnosed Diseases Program
Through our signature Undiagnosed Patient Program (UDP), the CCTS works with partners across the network to evaluate patients with chronic, undiagnosed diseases. By providing access to sophisticated DNA sequencing (whole genome and/or whole exome) and a multidisciplinary medical team, we help find answers for patients with rare or unusual conditions that have defied diagnosis. To date, 81 of the 201 patients evaluated by our UDP have been successfully diagnosed.